--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_MeanQualityByCycle.xml	Mon Jul 06 14:46:32 2015 -0400
@@ -0,0 +1,111 @@
+<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.135">
+  <description>chart distribution of base qualities</description>
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  <expand macro="requirements">
+    <requirement type="package" version="3.1.2">R</requirement>
+  </expand>
+  <command>
+    @java_options@
+    ##set up input files
+
+    #set $reference_fasta_filename = "localref.fa"
+    
+    #if str( $reference_source.reference_source_selector ) == "history":
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+    #else:
+        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+    #end if
+    
+    java -jar \$JAVA_JAR_PATH/picard.jar
+    MeanQualityByCycle
+    INPUT="${inputFile}"
+    OUTPUT="${outFile}"
+    CHART_OUTPUT="${pdfFile}"
+    REFERENCE_SEQUENCE="${reference_fasta_filename}"
+    ALIGNED_READS_ONLY="${aligned_reads_only}"
+    PF_READS_ONLY="${pf_reads_only}"
+  
+    ASSUME_SORTED="${assume_sorted}"
+    
+    VALIDATION_STRINGENCY="${validation_stringency}"
+    QUIET=true
+    VERBOSITY=ERROR
+  
+  </command>
+  <inputs>
+    <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
+    <conditional name="reference_source">
+      <param name="reference_source_selector" type="select" label="Load reference genome from">
+        <option value="cached">Local cache</option>
+        <option value="history">History</option>
+      </param>
+      <when value="cached">
+        <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
+          <options from_data_table="all_fasta">
+          </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
+      </when>
+    </conditional>
+    <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/>
+    <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
+    <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
+    
+    <expand macro="VS" />
+    
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
+    <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="assume_sorted" value="true" />
+      <param name="aligned_reads_only" value="false" />
+      <param name="pf_reads_only" value="false" />
+      <param name="reference_source_selector" value="history" />
+      <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" />
+      <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" />
+      <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
+    </test> 
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset. 
+
+@dataset_collections@
+
+@description@
+
+  ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value: 
+                                false. Possible values: {true, false} 
+
+  PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false. 
+                                This option can be set to 'null' to clear the default value. Possible values: {true, 
+                                false} 
+
+  ASSUME_SORTED=Boolean
+  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default: True 
+
+@more_info@
+
+  </help>
+</tool>
+
+